Systems and methods for analysis and interpretation of nucleic acid sequence data

ABSTRACT

Systems and method for annotating variants within a genome can call variants from reads or receive called variants directly and associate the called variants with functional annotations and interpretive annotations. A summary report of the called variants, the associated functional annotations, and the associated interpretive annotations can be generated.

RELATED APPLICATIONS

This application claims priority pursuant to 35 U.S.C. §119(e) to U.S.Provisional Patent Application Ser. No. 61/545,895, entitled “UserInterface for Analysis and Interpretation of Nucleic Acid SequenceData”, filed on Oct. 11, 2011, U.S. Provisional Patent Application Ser.No. 61/545,922, entitled “Systems and Methods for Analyzing andInterpreting Nucleic Acid Sequence Data”, filed on Oct. 11, 2011, U.S.Provisional Patent Application Ser. No. 61/598,499, entitled “Systemsand Methods for Analysis and Interpretation of Nucleic Acid SequenceData”, filed on Feb. 14, 2012, and U.S. Provisional Patent ApplicationSer. No. 61/640,389, entitled “Systems and Methods for Analysis andInterpretation of Nucleic Acid Sequence Data”, filed on Apr. 30, 2012,the entireties of which are incorporated herein by reference as if setforth in full.

FIELD

The present disclosure generally relates to nucleic acid sequence dataand in particular to user interfaces, systems and methods for annotatinggenomic variants detected in the nucleic acid sequence data.

INTRODUCTION

Upon completion of the Human Genome Project, one focus of the sequencingindustry has shifted to finding higher throughput and/or lower costnucleic acid sequencing technologies, sometimes referred to as “nextgeneration” sequencing (NGS) technologies. In making sequencing higherthroughput and/or less expensive, the goal is to make the technologymore accessible for sequencing. These goals can be reached through theuse of sequencing platforms and methods that provide sample preparationfor larger quantities of samples of significant complexity, sequencinglarger numbers of complex samples, and/or a high volume of informationgeneration and analysis in a short period of time. Various methods, suchas, for example, sequencing by synthesis, sequencing by hybridization,and sequencing by ligation are evolving to meet these challenges.

Research into fast and efficient nucleic acid (for example, genome,exome, etc.) sequence assembly methods is vital to the sequencingindustry as NGS technologies can provide ultra-high throughput nucleicacid sequencing. As such sequencing systems incorporating NGStechnologies can produce a large number of short sequence reads in arelatively short amount time. Sequence assembly methods must be able toassemble and/or map a large number of reads quickly and efficiently,such as by minimizing use of computational resources. For example, thesequencing of a human size genome can result in tens or hundreds ofmillions of reads that need to be assembled before they can be furtheranalyzed to determine their biological, diagnostic and/or therapeuticrelevance.

Exemplary applications of NGS technologies include, but are not limitedto: genomic variant (for example, indels, copy number variations, singlenucleotide polymorphisms, etc.) detection, resequencing, gene expressionanalysis and genomic profiling.

A wealth of nucleic acid sequence information is now available insequence databases, both public and private. For example, publicdatabases of metabolic, genetic and physiological pathways of variousorganisms (for example, Munich Information Center for Protein Sequences(MIPS), NCBI's Single Nucleotide Polymorphism database (dbSNP), etc.)and some genes (for example, Kyoto Encyclopedia of Genes and Genomes(KEGG), etc.) have been developed largely from the published literatureof many traditional low throughput experimental studies. An advantage ofthis abundance of data is that improved diagnostic testing and genomicsguided therapeutic regimens (for example, drugs, surgery, radiationtherapy, medical devices, diet, psychiatric therapy, etc.) will bepossible as new information about how an individuals' genetic andepigenetic profile correlates to risk factors for disease, drug targets,protein therapeutics, devices, treatment protocols, and the like areidentified and characterized. In addition, because relatively smalldifferences in the genetic makeup (genotype), gene expression, orepigenetic status of individuals can result in large differences inphysical characteristics (phenotype), some diagnostic testing andtherapeutic regimens may work better with some individuals than withothers, and in some cases deleterious effects can be avoided. Withknowledge of how different genotypes or other genetic and epigeneticfactors affect the function of a individual's various biologicalpathways (for example, metabolic, signaling, regulation, etc.),diagnostic tests and treatment regimens can potentially be customizedbased on genetic and epigenetic information associated with the specificindividual being treated.

While the quantity of nucleic acid sequence data that one can gatherusing conventional sequencing techniques is very large, it can often notbe presented or analyzed in the most useful context. The diagnostic andtherapeutic relevance of genetic and epigenetic data can often be bestdetermined by its relationship to other pieces of information. Forexample, knowing that a particular genetic mutation (for example, SNP,Indel, CNV, etc.) affects a particular metabolic or physiologicalpathway that plays a role in or otherwise affects the inception,progression, or treatment of a particular disease can be clinicallyimportant information. In addition, there is a need to correlate thisdata with various types of clinical data, for example, a patient's age,sex, weight, stage of clinical development, stage of diseaseprogression, etc.

Conventional techniques do not facilitate easy correlation of candidategene mutations with the wealth of information that is currentlyavailable that can provide functional or interpretive context to themutations. This is due to the enormous amount of information beinggenerated by researchers and the lack of adequate tools to organize theinformation in a manner which facilitates analysis of the same.

As such, there is a need for user friendly interfaces and methods toallow easy analysis and interpretation of genomic variant candidatesidentified in nucleic acid sequencing data.

DRAWINGS

For a more complete understanding of the principles disclosed herein,and the advantages thereof, reference is now made to the followingdescriptions taken in conjunction with the accompanying drawings, inwhich:

FIG. 1 is a block diagram that illustrates a computer system, inaccordance with various embodiments.

FIG. 2 is a schematic diagram of a system for reconstructing a nucleicacid sequence, in accordance with various embodiments.

FIG. 3 is a schematic diagram of a system for annotating genomicvariants, in accordance with various embodiments.

FIG. 4 is a depiction of the different kinds of functional typeannotations information that the functional annotations can annotatecalled variants with, in accordance with various embodiments.

FIG. 5 is an exemplary flowchart showing a method for annotating genomicvariants, in accordance with various embodiments.

FIG. 6 is an exemplary flowchart showing a method for annotating genomicvariants, in accordance with various embodiments.

FIG. 7 is an exemplary flowchart showing a method for configuring aworkflow, in accordance with various embodiments.

FIG. 8 is a diagram showing an exemplary interface for configuring aworkflow, in accordance with various embodiments.

FIG. 9 is a diagram showing an exemplary interface for configuring aquality control protocol, in accordance with various embodiments.

FIG. 10 is an exemplary flowchart showing a method for analyzing aspecimen, in accordance with various embodiments.

FIG. 11 is an exemplary flowchart showing a method for publishing areport, in accordance with various embodiments.

FIG. 12A is a diagram showing an exemplary interface for illustrating agene panel, in accordance with various embodiments.

FIG. 12B is a diagram showing an exemplary interface for selectingvariant filters, in accordance with various embodiments.

FIG. 13 is an exemplary flowchart showing a method for generatingreports, in accordance with various embodiments.

FIG. 14 is a diagram showing an exemplary interface for viewing statusinformation for an account, in accordance with various embodiments.

It is to be understood that the figures are not necessarily drawn toscale, nor are the objects in the figures necessarily drawn to scale inrelationship to one another. The figures are depictions that areintended to bring clarity and understanding to various embodiments ofapparatuses, systems, and methods disclosed herein. Wherever possible,the same reference numbers will be used throughout the drawings to referto the same or like parts. Moreover, it should be appreciated that thedrawings are not intended to limit the scope of the present teachings inany way.

DESCRIPTION OF VARIOUS EMBODIMENTS

Embodiments of user interfaces and methods for analyzing andinterpreting nucleic acid sequence data are described herein.

The section headings used herein are for organizational purposes onlyand are not to be construed as limiting the described subject matter inany way.

In this detailed description of the various embodiments, for purposes ofexplanation, numerous specific details are set forth to provide athorough understanding of the embodiments disclosed. One skilled in theart will appreciate, however, that these various embodiments may bepracticed with or without these specific details. In other instances,structures and devices are shown in block diagram form. Furthermore, oneskilled in the art can readily appreciate that the specific sequences inwhich methods are presented and performed are illustrative and it iscontemplated that the sequences can be varied and still remain withinthe spirit and scope of the various embodiments disclosed herein.

All literature and similar materials cited in this application,including but not limited to, patents, patent applications, articles,books, treatises, and internet web pages are expressly incorporated byreference in their entirety for any purpose. Unless defined otherwise,all technical and scientific terms used herein have the same meaning asis commonly understood by one of ordinary skill in the art to which thevarious embodiments described herein belongs. When definitions of termsin incorporated references appear to differ from the definitionsprovided in the present teachings, the definition provided in thepresent teachings shall control.

It will be appreciated that there is an implied “about” prior to thetemperatures, concentrations, times, number of bases, coverage, etc.discussed in the present teachings, such that slight and insubstantialdeviations are within the scope of the present teachings. In thisapplication, the use of the singular includes the plural unlessspecifically stated otherwise. Also, the use of “comprise”, “comprises”,“comprising”, “contain”, “contains”, “containing”, “include”,“includes”, and “including” are not intended to be limiting. It is to beunderstood that both the foregoing general description and the followingdetailed description are exemplary and explanatory only and are notrestrictive of the present teachings.

Further, unless otherwise required by context, singular terms shallinclude pluralities and plural terms shall include the singular.Generally, nomenclatures utilized in connection with, and techniques of,cell and tissue culture, molecular biology, and protein and oligo- orpolynucleotide chemistry and hybridization described herein are thosewell known and commonly used in the art. Standard techniques are used,for example, for nucleic acid purification and preparation, chemicalanalysis, recombinant nucleic acid, and oligonucleotide synthesis.Enzymatic reactions and purification techniques are performed accordingto manufacturer's specifications or as commonly accomplished in the artor as described herein. The techniques and procedures described hereinare generally performed according to conventional methods well known inthe art and as described in various general and more specific referencesthat are cited and discussed throughout the instant specification. See,for example, Sambrook et al., Molecular Cloning: A Laboratory Manual(Third ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor,N.Y. 2000). The nomenclatures utilized in connection with, and thelaboratory procedures and techniques described herein are those wellknown and commonly used in the art.

As used herein, “a” or “an” means “at least one” or “one or more.”

A “system” may be used to denote a set of components, real or abstract,comprising a whole where each component interacts with or is related toat least one other component within the whole.

A “biomolecule” may be used to denote any molecule that is produced by abiological organism, including large polymeric molecules such asproteins, polysaccharides, lipids, and nucleic acids (DNA and RNA) aswell as small molecules such as primary metabolites, secondarymetabolites, and other natural products.

The phrase “next generation sequencing” or NGS refers to sequencingtechnologies having increased throughput as compared to traditionalSanger- and capillary electrophoresis-based approaches, for example withthe ability to generate hundreds of thousands of relatively smallsequence reads at a time. Some examples of next generation sequencingtechniques include, but are not limited to, sequencing by synthesis,sequencing by ligation, and sequencing by hybridization. Morespecifically, the Personal Genome Machine (PGM) of Life TechnologiesCorp. provides massively parallel sequencing with enhanced accuracy. ThePGM System and associated workflows, protocols, chemistries, etc. aredescribed in more detail in U.S. Patent Application Publication No.2009/0127589 and No. 2009/0026082, the entirety of each of theseapplications being incorporated herein by reference.

The phrase “sequencing run” refers to any step or portion of asequencing experiment performed to determine some information relatingto at least one biomolecule (for example, nucleic acid molecule).

It is well known that DNA (deoxyribonucleic acid) is a chain ofnucleotides consisting of 4 types of nucleotides; A (adenine), T(thymine), C (cytosine), and G (guanine), and that RNA (ribonucleicacid) is comprised of 4 types of nucleotides; A, U (uracil), G, and C.It is also known that certain pairs of nucleotides specifically bind toone another in a complementary fashion (called complementary basepairing). That is, adenine (A) pairs with thymine (T) (in the case ofRNA, however, adenine (A) pairs with uracil (U)), and cytosine (C) pairswith guanine (G). When a first nucleic acid strand binds to a secondnucleic acid strand made up of nucleotides that are complementary tothose in the first strand, the two strands bind to form a double strand.As used herein, “nucleic acid sequencing data,” “nucleic acid sequencinginformation,” “nucleic acid sequence,” “genomic sequence,” “geneticsequence,” or “fragment sequence,” or “nucleic acid sequencing read”denotes any information or data that is indicative of the order of thenucleotide bases (for example, adenine, guanine, cytosine, andthymine/uracil) in a molecule (for example, whole genome, wholetranscriptome, exome, oligonucleotide, polynucleotide, fragment, etc.)of DNA or RNA. It should be understood that the present teachingscontemplate sequence information obtained using all available varietiesof techniques, platforms or technologies, including, but not limited to:capillary electrophoresis, microarrays, ligation-based systems,polymerase-based systems, hybridization-based systems, direct orindirect nucleotide identification systems, pyrosequencing, ion- orpH-based detection systems, electronic signature-based systems, etc.

The phrase “base space” refers to a nucleic acid sequence data schemawhere nucleic acid sequence information is represented by the actualnucleotide base composition of the nucleic acid sequence. For example,the nucleic acid sequence “ATCGA” is represented in base space by theactual nucleotide base identities (for example, A, T/or U, C, G) of thenucleic acid sequence.

The phrase “flow space” refers to a nucleic acid sequence data schemawherein nucleic acid sequence information is represented by nucleotidebase identifications (or identifications of known nucleotide base flows)coupled with signal or numerical quantification componentsrepresentative of nucleotide incorporation events for the nucleic acidsequence. The quantification components may be related to the relativenumber of continuous base repeats, such as homopolymers, whoseincorporation is associated with a respective nucleotide base flow. Forexample, the nucleic acid sequence “ATTTGA” may be represented by thenucleotide base identifications A, T, G and A (based on the nucleotidebase flow order) plus a quantification component for the various flowsindicating base presence/absence as well as possible existence ofhomopolymers. Thus for “T” in the example sequence above, thequantification component may correspond to a signal or numericalidentifier of greater magnitude than would be expected for a single “T”and may be resolved to indicate the presence of a homopolymer stretch of“T”s (in this case a 3-mer) in the “ATTTGA” nucleic acid sequence.

A “polynucleotide”, “nucleic acid”, or “oligonucleotide” refers to alinear polymer of nucleosides (including deoxyribonucleosides,ribonucleosides, or analogs thereof) joined by internucleosidiclinkages. Typically, a polynucleotide comprises at least threenucleosides. Usually oligonucleotides range in size from a few monomericunits, for example 3-4, to several hundreds of monomeric units. Whenevera polynucleotide such as an oligonucleotide is represented by a sequenceof letters, such as “ATGCCTG,” it will be understood that thenucleotides are in 5′->3′ order from left to right and that “A” denotesdeoxyadenosine, “C” denotes deoxycytidine, “G” denotes deoxyguanosine,and “T” denotes thymidine, unless otherwise noted. The letters A, C, G,and T may be used to refer to the bases themselves, to nucleosides, orto nucleotides comprising the bases, as is standard in the art.

The phrase “genomic variants” or “genome variants” denote a single or agrouping of sequences (in DNA or RNA) that have undergone changes asreferenced against a particular species or sub-populations within aparticular species due to mutations, recombination/crossover or geneticdrift. Examples of types of genomic variants include, but are notlimited to: single nucleotide polymorphisms (SNPs), copy numbervariations (CNVs), insertions/deletions (Indels), inversions, etc.

Genomic variants can be identified using a variety of techniques,including, but not limited to: array-based methods (for example, DNAmicroarrays, etc.) and whole or targeted nucleic acid sequencing. Withnucleic acid sequencing, coverage data can be available at single baseresolution. Nucleic acid sequencing systems such as the LifeTechnologies/Ion Torrent Personal Genome Machine (PGM) and AppliedBiosystems SOLID™ Sequencing System can be used to sequence nucleic acidsamples (for example human tissue/cell samples) which can include a test(or candidate) sample and a reference (or normal) sample.

In various embodiments, genomic variants can be detected using a nucleicacid sequencing system and/or analysis of sequencing data. Thesequencing workflow can begin with the test sample being sheared ordigested into hundreds, thousands or millions of smaller fragments whichare sequenced on a nucleic acid sequencer to provide hundreds, thousandsor millions of sequence reads, such as nucleic acid sequence reads. Eachread can then be mapped to a reference or target genome, and in the caseof mate-pair fragments, the reads can be paired thereby allowinginterrogation of repetitive regions of the genome. The results ofmapping and pairing can be used as input for various standalone orintegrated genome variant (for example, SNP, CNV, Indel, inversion,etc.) analysis tools.

When genome variants are initially identified in nucleic acid samples,especially during analysis of disease-associated genes, their functionalimplications might not be immediately evident. Distinguishing between agenomic variant that changes the phenotype and one that does not is adifficult task. An increasing amount of evidence indicates that genomicvariants in both coding and non-coding sequences can have unexpecteddeleterious effects on the splicing of a gene transcript. This makesdistinguishing between benign polymorphisms and disease-associatedsplicing mutations difficult. Therefore, the ability to link the geneticvariants identified in a nucleic acid sequence to various pieces ofrelevant biological information can greatly assist in the determinationof the biological significance of the identified genetic variants.

The phrase “functional annotation” denotes data and information that canbe relevant to the role that a called variant plays ingene/transcript/protein level function.

The phrase “coding region” denotes the portion of a gene's DNA or RNA,composed of exons that codes for protein. It should be understood,however, that the coding region of mRNA does not typically include thefirst part of the first exon (the 5′ untranslated region) or the lastpart of the last exon (the 3′ untranslated region).

The phrase “intragenic region,” “intronic region,” or “intron” denotesany nucleotide sequence within a gene that is removed by RNA splicing togenerate the final mature RNA product of a gene.

The phrase “intergenic region” denotes a stretch of DNA sequenceslocated between genes that contain few or no genes.

The phrase “sample genome” can denote a whole or partial genome of anorganism.

The techniques of “paired-end,” “pairwise,” “paired tag,” or “mate pair”sequencing are generally known in the art of molecular biology (SiegelA. F. et al., Genomics. 2000, 68: 237-246; Roach J. C. et al., Genomics.1995, 26: 345-353). These sequencing techniques can allow thedetermination of multiple “reads” of sequence, each from a differentplace on a single polynucleotide. Typically, the distance between thetwo reads, such as the insert region, or other information regarding arelationship between the reads is known. In some situations, thesesequencing techniques provide more information than does sequencing twostretches of nucleic acid sequences in a random fashion. With the use ofappropriate software tools for the assembly of sequence information (forexample, Millikin S. C. et al., Genome Res. 2003, 13: 81-90; Kent, W. J.et al., Genome Res. 2001, 11: 1541-8) it is possible to make use of theknowledge that the “paired-end,” “pairwise,” “paired tag” or “mate pair”sequences are not completely random, but are known to occur a knowndistance apart and/or to have some other relationship, and are thereforelinked or paired in the genome. This information can aid in the assemblyof whole nucleic acid sequences into a consensus sequence.

Computer-Implemented System

FIG. 1 is a block diagram that illustrates a computer system 100, uponwhich embodiments of the present teachings may be implemented. Invarious embodiments, computer system 100 can include a bus 102 or othercommunication mechanism for communicating information, and a processor104 coupled with bus 102 for processing information. In variousembodiments, computer system 100 can also include a memory 106, whichcan be a random access memory (RAM) or other dynamic storage device,coupled to bus 102 for determining base calls, and instructions to beexecuted by processor 104. Memory 106 also can be used for storingtemporary variables or other intermediate information during executionof instructions to be executed by processor 104. In various embodiments,computer system 100 can further include a read only memory (ROM) 108 orother static storage device coupled to bus 102 for storing staticinformation and instructions for processor 104. A storage device 110,such as a magnetic disk or optical disk, can be provided and coupled tobus 102 for storing information and instructions.

In various embodiments, computer system 100 can be coupled via bus 102to a display 112, such as a cathode ray tube (CRT) or liquid crystaldisplay (LCD), for displaying information to a computer user. An inputdevice 114, including alphanumeric and other keys, can be coupled to bus102 for communicating information and command selections to processor104. Another type of user input device is a cursor control 116, such asa mouse, a trackball or cursor direction keys for communicatingdirection information and command selections to processor 104 and forcontrolling cursor movement on display 112. This input device typicallyhas two degrees of freedom in two axes, a first axis (for example, x)and a second axis (for example, y), that allows the device to specifypositions in a plane.

A computer system 100 can perform the present teachings. Consistent withcertain implementations of the present teachings, results can beprovided by computer system 100 in response to processor 104 executingone or more sequences of one or more instructions contained in memory106. Such instructions can be read into memory 106 from anothercomputer-readable medium, such as storage device 110. Execution of thesequences of instructions contained in memory 106 can cause processor104 to perform the processes described herein. Alternatively hard-wiredcircuitry can be used in place of or in combination with softwareinstructions to implement the present teachings. Thus implementations ofthe present teachings are not limited to any specific combination ofhardware circuitry and software.

The term “computer-readable medium” as used herein refers to any mediathat participates in providing instructions to processor 104 forexecution. Such a medium can take many forms, including but not limitedto, non-volatile media, volatile media, and transmission media. Examplesof non-volatile media can include, but are not limited to, optical ormagnetic disks, such as storage device 110. Examples of volatile mediacan include, but are not limited to, dynamic memory, such as memory 106.Examples of transmission media can include, but are not limited to,coaxial cables, copper wire, and fiber optics, including the wires thatcomprise bus 102.

Common forms of computer-readable media include, for example, a floppydisk, a flexible disk, hard disk, magnetic tape, or any other magneticmedium, a CD-ROM, any other optical medium, punch cards, paper tape, anyother physical medium with patterns of holes, a RAM, PROM, and EPROM, aFLASH-EPROM, any other memory chip or cartridge, or any other tangiblemedium from which a computer can read.

In accordance with various embodiments, instructions configured to beexecuted by a processor to perform a method are stored on acomputer-readable medium. The computer-readable medium can be a devicethat stores digital information. For example, a computer-readable mediumincludes a compact disc read-only memory (CD-ROM) as is known in the artfor storing software. The computer-readable medium is accessed by aprocessor suitable for executing instructions configured to be executed.

Nucleic Acid Sequencing Platforms

Nucleic acid sequence data can be generated using various techniques,platforms or technologies, including, but not limited to: capillaryelectrophoresis, microarrays, ligation-based systems, polymerase-basedsystems, hybridization-based systems, direct or indirect nucleotideidentification systems, pyrosequencing, ion- or pH-based detectionsystems, electronic signature-based systems, fluorescent-based detectionsystems, single molecule methods, etc.

Various embodiments of nucleic acid sequencing platforms, such as anucleic acid sequencer, can include components as displayed in the blockdiagram of FIG. 2. According to various embodiments, sequencinginstrument 200 can include a fluidic delivery and control unit 202, asample processing unit 204, a signal detection unit 206, and a dataacquisition, analysis and control unit 208. Various embodiments ofinstrumentation, reagents, libraries and methods used for nextgeneration sequencing are described in U.S. Patent ApplicationPublication No. 2009/0127589 and No. 2009/0026082 are incorporatedherein by reference. Various embodiments of instrument 200 can providefor automated sequencing that can be used to gather sequence informationfrom a plurality of sequences in parallel, such as substantiallysimultaneously.

In various embodiments, the fluidics delivery and control unit 202 caninclude reagent delivery system. The reagent delivery system can includea reagent reservoir for the storage of various reagents. The reagentscan include RNA-based primers, forward/reverse DNA primers,oligonucleotide mixtures for ligation sequencing, nucleotide mixturesfor sequencing-by-synthesis, optional ECC oligonucleotide mixtures,buffers, wash reagents, blocking reagent, stripping reagents, and thelike. Additionally, the reagent delivery system can include a pipettingsystem or a continuous flow system which connects the sample processingunit with the reagent reservoir.

In various embodiments, the sample processing unit 204 can include asample chamber, such as flow cell, a substrate, a micro-array, amulti-well tray, or the like. The sample processing unit 204 can includemultiple lanes, multiple channels, multiple wells, or other means ofprocessing multiple sample sets substantially simultaneously.Additionally, the sample processing unit can include multiple samplechambers to enable processing of multiple runs simultaneously. Inparticular embodiments, the system can perform signal detection on onesample chamber while substantially simultaneously processing anothersample chamber. Additionally, the sample processing unit can include anautomation system for moving or manipulating the sample chamber.

In various embodiments, the signal detection unit 206 can include animaging or detection sensor. For example, the imaging or detectionsensor can include a CCD, a CMOS, an ion sensor, such as an ionsensitive layer overlying a CMOS, a current detector, or the like. Thesignal detection unit 206 can include an excitation system to cause aprobe, such as a fluorescent dye, to emit a signal. The expectationsystem can include an illumination source, such as arc lamp, a laser, alight emitting diode (LED), or the like. In particular embodiments, thesignal detection unit 206 can include optics for the transmission oflight from an illumination source to the sample or from the sample tothe imaging or detection sensor. Alternatively, the signal detectionunit 206 may not include an illumination source, such as for example,when a signal is produced spontaneously as a result of a sequencingreaction. For example, a signal can be produced by the interaction of areleased moiety, such as a released ion interacting with an ionsensitive layer, or a pyrophosphate reacting with an enzyme or othercatalyst to produce a chemiluminescent signal. In another example,changes in an electrical current can be detected as a nucleic acidpasses through a nanopore without the need for an illumination source.

In various embodiments, data acquisition analysis and control unit 208can monitor various system parameters. The system parameters can includetemperature of various portions of instrument 200, such as sampleprocessing unit or reagent reservoirs, volumes of various reagents, thestatus of various system subcomponents, such as a manipulator, a steppermotor, a pump, or the like, or any combination thereof.

It will be appreciated by one skilled in the art that variousembodiments of instrument 200 can be used to practice variety ofsequencing methods including ligation-based methods, sequencing bysynthesis, single molecule methods, nanopore sequencing, and othersequencing techniques.

In various embodiments, the sequencing instrument 200 can determine thesequence of a nucleic acid, such as a polynucleotide or anoligonucleotide. The nucleic acid can include DNA or RNA, and can besingle stranded, such as ssDNA and RNA, or double stranded, such asdsDNA or a RNA/cDNA pair. In various embodiments, the nucleic acid caninclude or be derived from a fragment library, a mate pair library, aChIP fragment, or the like. In particular embodiments, the sequencinginstrument 200 can obtain the sequence information from a single nucleicacid molecule or from a group of substantially identical nucleic acidmolecules.

In various embodiments, sequencing instrument 200 can output nucleicacid sequencing read data in a variety of different output data filetypes/formats, including, but not limited to: *.fasta, *.csfasta,*seq.txt, *qseq.txt, *.fastq, *.sff, *prb.txt, *.sms, *srs and/or *.qv.

Genomic Variant Annotation System

Systems and methods for annotating biological information withfunctional and/or interpretive information are disclosed. Theannotations can provide commentary or explanatory notes related to thebiological information. The biological information can include sequenceinformation, genomic variants (for example, SNPs, Indels, CNVs,inversions, etc.) identified from analyzing nucleic acid sequence data,and the like. That is, the various embodiments disclosed herein canutilize external sources of information (for example, annotation datasources and manually entered comments or information) to associateinformation that may be helpful in understanding or interpreting theconsequences of biological information on cell function, diseaseprogression, therapeutic efficacy, inherited traits, etc. Theannotations can include information relating to intron-exon boundaries,regulatory sequences, repeats, gene names, and protein products that arerelevant to the identified biological information, as well as relatingthe biological information to clinical and research results andoutcomes.

Examples of annotation sources, include, but are not limited to genetransport format (GTF) database from RefGene database/NCBI (used todetermine whether a variant overlaps a gene or exon), the dbSNPdatabase/National Center for Biotechnology Information (NCBI) (containsinformation on SNPs and indels already found by other studies), Genome10K, The Cancer Genome Atlas, etc. These annotations can be useful inhelping to determine the potential functional consequences of theidentified genomic variant.

FIG. 3 is a schematic diagram of a system for annotating genomicvariants, in accordance with various embodiments.

As depicted herein, annotation system 300 can include a nucleic acidsequence analysis device 304 (for example, nucleic acid sequencer,real-time/digital/quantitative PCR instrument, microarray scanner,etc.), an analytics computing server/node/device 302, a display 338and/or a client device terminal 336, and one or more public 330 andproprietary 332 annotations content sources.

In various embodiments, the analytics computing sever/node/device 302can be communicatively connected to the nucleic acid sequence analysisdevice 304, client device terminal 336, public annotations contentsource 330 and/or proprietary annotations content source 332 via anetwork connection 334 that can be either a “hardwired” physical networkconnection (for example, Internet, LAN, WAN, VPN, etc.) or a wirelessnetwork connection (for example, Wi-Fi, WLAN, etc.).

In various embodiments, the analytics computing device/server/node 302can be a workstation, mainframe computer, distributed computing node(part of a “cloud computing” or distributed networking system), personalcomputer, mobile device, etc. In various embodiments, the nucleic acidsequence analysis device 304 can be a nucleic acid sequencer,real-time/digital/quantitative PCR instrument, microarray scanner, etc.It should be understood, however, that the nucleic acid sequenceanalysis device 304 can essentially be any type of instrument that cangenerate nucleic acid sequence data from samples obtained from anindividual 306.

The analytics computing server/node/device 302 can be configured to hosta mapping engine 308, a variant calling engine 310, a decision supportmodule 312 and a reporter module 316.

The mapping engine 308 can be configured to align or map a query nucleicacid sequence read to a reference sequence. Generally, the length of thesequence read is substantially less than the length of the referencesequence. In reference sequence mapping/alignment, sequence reads can beassembled against an existing backbone sequence (for example, referencesequence, etc.) to build a sequence that is similar but not necessarilyidentical to the backbone sequence. Once a backbone sequence is foundfor an organism, comparative sequencing or re-sequencing can be used tocharacterize the genetic diversity within the organism's species orbetween closely related species. In various embodiments, the referencesequence can be a whole/partial genome, whole/partial exome,whole/partial transcriptome, etc.

In various embodiments, the sequence read and reference sequence can berepresented as a sequence of nucleotide base symbols in base space. Invarious embodiments, the sequence read and reference sequence can berepresented as one or more color symbols in color space. In variousembodiments, the sequence read and reference sequence can be representedas nucleotide base symbols with signal or numerical quantitationcomponents in flow space.

In various embodiments, the alignment of the sequence read and referencesequence can include a limited number of mismatches between the basesthat comprise the sequence read and the bases that comprise thereference sequence. Generally, at least a portion of the sequence readcan be aligned to a portion of the reference sequence, such as areference nuclear genome, a reference mitochondrial genome, a referenceprokaryotic genome, a reference chloroplast genome, or the like, inorder to minimize the number of mismatches between the sequence fragmentand the reference sequence.

The variant calling engine 310 can be configured to receive mappedsequence reads from the mapping engine 308 and analyze the mapped readsto detect and call or identify one or more variants within the reads.Examples of variants that can be called by a variant calling engine 310include but are not limited to: single nucleotide polymorphisms (SNP),nucleotide insertions or deletions (indels), copy number variations(CNV) identification, inversion polymorphims, and the like. The variantschanges to transcript or expression levels, etc. The variants caninclude mutations within a coding region that alter an expressed aminoacid sequence, mutations that affect the rate of translation,maturation, or transport of a protein, mutations that affect mRNAsplicing, mutations that affect the rate of transcription or thestability of an RNA, mutations that affect chromatin remodeling, or thelike.

The reporter module 316 can be in communications with the decisionsupport module 312 and be configured to generate a summary report of thecalled genomic variants that have been annotated by the annotatorcomponent 314 that can be part of the decision support module 312.

The decision support module can include an annotator component 314, avariome data store 322, an annotations data store 324, a filteringcomponent 328 and/or an annotations importer component 326. In variousembodiments, the annotator component 314 can be in communication withthe variant calling engine 310, the variome data store 322 and/or theannotations data store 324. That is, the annotator component 314 canrequest and receive data and information (through, for example, datastreams, data files, text files, etc.) from variant calling engine 310,variome data store 322 and annotations data store 324. In variousembodiments, the variant calling engine 310 can be configured tocommunicate variants called for a sample genome in various formats, suchas, but not limited to, variant call format (VCF), generic featureformat (GFF) heirachical data format (HDF), genome variation format(GVF), or HL7 formatted data. It should be understood, however, that thecalled variants can be communicated using any file format where thecalled variant information can be parsed and/or extracted for laterprocessing/analysis.

The variome data store 322 can be configured to store the variant callsreceived from the variant calling engine 310 and/or the annotatorcomponent 314 in a format that is accessible for mining.

That is, the called variant data can be maintained as a database orinstantiated in some other persistent (and queryable) electronic form inthe device memory (for example, hard drive, RAM, ROM, etc.) of theanalytics computing server/node/device 302. The called variant data canbe structured and use a common syntax and semantic model throughout orinclude appropriate interpreters between formats that allow forone-to-one mapping between terms and data types. In various embodiments,the variome data store 322 can be an indexed database table of variants.In particular embodiments, the indexed database can be configured forfast querying and filtering operations.

The annotations data store 324 can be in communications with theannotations importer component 326 and be configured to store data andinformation that can be used by the annotator component 314 to annotatethe called variants. That is, the annotations data store 324 can storeannotation data and information that can be relevant to the role thatthe called variant plays in the function, such as at a chromosome level,gene level, a transcript level, a protein level, or the like, (forexample, functional type annotations) and/or the biological impact (forexample, interpretive type annotations) of the called variants. Invarious embodiments, functional type annotations can include, but arenot limited to: locus classification of the called variant, proteinfunction impact score of the called variant, amino acid changesresulting from the called variant, gene/transcripts affected by thecalled variant, etc. In various embodiments, interpretive typeannotations can include, but are not limited to: disease states orsusceptibility to a disease (for example, cancer, diabetes,hypertension, heart disease, etc.) associated with the called variant,impacts that the called variant has on a particular therapeutic regimen(for example, drugs, surgical options, medical device, psychiatrictherapy, lifestyle changes, drug sensitivities, etc.), presence of thevariant on a list of annotated variants, etc. For example, a SNP variantcall can be annotated with functional type annotations that point to thetranscripts that the called SNP impacts and interpretive typeannotations that are directed to diagnosing a particular disease stateor a susceptibility to a disease.

The annotations importer component 326 can be configured to receiveannotations content from one or more public 330 or proprietary 332annotations content sources and convert the annotations content into aformat that can be stored in the annotations data store 324 and isaccessible for mining. That is, the annotations importer component 326can convert annotations data and/or information into a format that canbe stored onto a database or instantiated in some other persistent (andqueryable) electronic form in the device memory (for example, harddrive, RAM, ROM, etc.) of the analytics computing server/node/device302.

In various embodiments, annotations content can be manually entered oruploaded by a user to the annotations importer component 326 via acomputer readable storage medium that is communicatively connected (forexample, via a serial data bus connection, parallel data bus connection,internet/intranet network connection, etc.) to the analytics computingserver/node/device 302. That is, a user can selectively uploadannotations content to the annotations data store 324 depending on therequirements of the particular application. Examples of computerreadable medium include, but are not limited to: hard drives, networkattached storage (NAS), read-only memory, random-access memory, CD-ROMs,CD-Rs, CD-RWs, magnetic tapes, FLASH memory and otheroptical/non-optical data storage devices.

In various embodiments, annotations content can be automaticallyrequested and sent from public 330 and/or proprietary 332 annotationscontent sources to the annotations importer component 326 through theuse of a data refresh executable or script. That is, the annotationscontent in the annotations data store 324 can be continuously refreshedas the public 330 and/or proprietary 332 annotations content sources areupdated with new or modified annotations content.

In various embodiments, the annotator component 314 can include afunctional annotations engine 318 and interpretive annotations engine320.

The functional annotations engine 318 can be configured to receivecalled variants from the variome data store 322, associate one or morefunctional type annotations (stored in the annotations data store 324)to the called variants and update the called variant records in thevariome data store 322 with the associated functional type annotations.In various embodiments, the functional annotations engine 318 can beconfigured to annotate all called variants that fall within a block ofoverlapping transcripts (in the sample genome) at the same time. Thatis, the functional annotations engine 318 can group overlappingtranscripts together into a “gene block” and then annotate all variantsin the gene block together. The advantage here is that all calledvariants that are potentially mutually interacting can be grouped andannotated together to give researchers/clinicians greater insight intothe synergistic or antagonistic interplay between variants.

In various embodiments, the functional annotations engine 318 can beselectively configured to annotate only called variants that fall withina coding region (for example, exons, codons) of the sample genome beingannotated. In various embodiments, the functional annotations engine 318can be selectively configured to annotate only called variants that fallwithin an intragenic region, such as an intron, of the sample genomebeing annotated. In various embodiments, the functional annotationsengine 318 can be selectively configured to annotate only the calledvariants in the intergenic region of the sample genome being annotated.

In various embodiments, the functional annotations engine 318 canreceive the called variants in the form of a called variant data file(for example, *.vcf or other file format), associate the functional typeannotations, and store the variants and annotations to the variome datastore 322. In various embodiments, the functional annotations engine 318can receive the called variants as variant data (for example, variantbase identity and genome position, etc.), associates one or morefunctional type annotations to the called variant and directly updatesthe called variant record in the variome data store 322 with theassociated functional type annotations information. That is, thefunctional annotations engine 318 can receive called variants directlyfrom the variome data store 322, annotate them and save them back on thevariome data store 322 or alternate data store.

As shown in FIG. 4, the functional annotations engine 318 can annotatethe called variants with several different kinds of functional typeannotations information. In various embodiments, the functionalannotations engine 318 can be configured to first annotate the calledvariants with information, such as which transcripts they are associatedwith using “gene model” information 402 from one or more public orproprietary sources (for example, refGene, Ensembl, etc.). That is,applying gene transcript information from a “gene model” to the calledvariant to provide information about which transcripts that the calledvariant is found in (or impacts). Typically, the gene model selected isfrom the same species as the organism that supplied the sample genomethat is being analyzed. It should be understood, however, that incertain applications it may be instructive to a researcher or clinicianto annotate called variants against the gene models of other species.

In various embodiments, the functional annotations can also beconfigured to map the coding regions, such as exons, of the transcriptswhich are associated with each called variant to a reference genome 404to obtain base information about the codons. That is, the base sequenceinformation provided by the reference genome can be used to fill in thebase information for the actual codons where the called variants arefound and/or in the transcripts the called variant are found.

In various embodiments, the functional annotations engine 318 can beconfigured to associate a protein function impact score 406 to eachcalled variant using one or more public or proprietary modelingtools/algorithms (for example, POLYPHEN, SIFT, Grantham, GERP, etc.).The scores can predict the likelihood that a called variant which causesan amino acid substitution will have a deleterious effect on thestructure and function of a human protein.

The interpretive annotations engine 320 can be configured to receivecalled variants from the variome data store 322, associate one or moreinterpretive type annotations (stored in the annotations data store 324)to the called variants and update the called variant records in thevariome data store 322 with the associated interpretive typeannotations.

In various embodiments, the interpretive annotations engine 320 receivesthe called variants in the form of a called variant data file (forexample, *.vcf or other file format), associate the interpretive typeannotations, and store the variants and annotations to the variome datastore 322. In various embodiments, the interpretive annotations engine318 receives the called variants as variant data (for example, variantbase identity and genome position, etc.), associates one or moreinterpretive type annotations to the called variant and directly updatesthe called variant record in the variome data store 322 with theassociated interpretive type annotations information.

In various embodiments, the interpretive annotations engine 320 can beselectively configured to annotate called variants in the sample genomebeing annotated. In various embodiments, the interpretive annotationsengine 320 can be selectively configured to annotate called variantsthat fall within a coding region (for example, exons, codons) of thesample genome being annotated. In various embodiments, the interpretiveannotations engine 320 can be selectively configured to annotate calledvariants that fall within an intragenic region, such as an intron, ofthe sample genome being annotated. In various embodiments, theinterpretive annotations engine 320 can be selectively configured toannotate the called variants in the intergenic region of the samplegenome being annotated.

In various embodiments, annotator component 314 can provide the variantsto a third party annotation source, such as Public Annotations Content330 or Proprietary Annotations Content 332 for annotation orinterpretation. The third party annotation source can provide functionalor interpretive annotations back to annotator component 314, and theannotations can be stored within Variome Data Store 322.

In various embodiments, the system can be configured to automate theprocessing of sample data. For example, a workflow can be selected todefine how the data is processed by the mapping engine 308, the variantcalling engine 310, and the annotator component 314. In particularembodiments, a workflow can be selected when setting up the run on thenucleic acid sequence analysis device 304 and the data can beautomatically uploaded to the analytics computing device 302.Additionally, the workflow can be automatically launched when the datahas been uploaded. In other embodiments, the data can be uploaded,manually or automatically, from the nucleic acid sequence analysisdevice 304 and the workflow can be selected and launched manually.Generally, once the workflow has been selected and launched, analysiscan proceed from through the mapping engine 308, the variant callingengine, 310, and the annotator component 314 without furtherintervention by a user.

The filtering component 328 can be configured to allow a user to setfilter conditions to filter out the called variants that are included inthe summary report generated by the reporter module 316. Examples offilter conditions include, but are not limited to, filtering for:variants that are non-synonomous and fall within a particular gene,variants that are associated with a particular disease condition,variants that have a functional score of greater or less than a selectedvalue, novel variants that are not present in a functional typeannotations source, variants that fall in gene panel regions (defined byuser), etc. In various embodiments, the filtering component 328 canutilize combinations of filters, such as for example filtering forvariants that fall within a particular gene and have a functional scoreindicative of a significant effect.

In various embodiments, the filtering component 328 can be configuredwith a collection of filters to select for variants with a highlikelihood of having possible functional significance. For example, thefiltering component 328 can select for missense mutations and nonsensemutations and exclude synonymous mutations. Additionally, the filteringcomponent 328 can select for novel variants or clinically significantvariants and exclude variants that have been identified to have limitedfunctional or clinical significance. Novel variants can include variantsthat are not included in the annotations data store, variants that havenot previously been classified as to their clinical or functionalsignificance, or the like. Further, the filtering component 328 canselect for variants that have a significant effect on the structure orstability of a protein and exclude variants that have a minimal effecton the protein, such as based on, for example, a function SIFT score.Still further, the filtering component 328 can select for variants thataffect allele frequency. Also, the filtering component 328 may select orexclude variants at positions of known significance, such as positionsknown to have a high incidence of mutation in cancers, positions with alow or high number of false positive variant calls, positions known tohave a minimal functional impact, or the like.

In various embodiments, the variome data 322 and the annotations data324 stores can be combined into a single data store configured to storeboth called variant data and variant annotations information.

Client terminal 336 can be a thin client or thick client computingdevice. In various embodiments, client terminal 336 can have a webbrowser (for example, INTERNET EXPLORER™, FIREFOX™, SAFARI™, etc) thatcan be used to communicate information to and/or control the operationof the mapping engine 308, variant calling engine 310, decision supportmodule 312, annotator component 314, filtering component 328,annotations importer component 326, variome data store 322, annotationsdata store 324, functional annotations engine 318 and/or interpretiveannotations engine 320 using a browser to control their function. Forexample, the client terminal 336 can be used to configure the operatingparameters (for example, match scoring parameters, annotationsparameters, filtering parameters, data security and retentionparameters, etc.) of the various modules, depending on the requirementsof the particular application. Similarly, client terminal 336 can alsobe configured to display the results of the analysis performed by thedecision support module 312 and the nucleic acid sequencer 304.

It should be understood that the various data stores disclosed as partof system 300 can represent hardware-based storage devices (for example,hard drive, flash memory, RAM, ROM, network attached storage, etc.) orinstantiations of a database stored on a standalone or networkedcomputing device(s).

It should also be appreciated that the various data stores andmodules/engines shown as being part of the system 300 can be combined orcollapsed into a single module/engine/data store, depending on therequirements of the particular application or system architecture.Moreover, in various embodiments, the system 300 can comprise additionalmodules, engines, components or data stores as needed by the particularapplication or system architecture or to extend functionality.

In various embodiments, the system 300 can be configured to process thenucleic acid reads in color space. In various embodiments, system 300can be configured to process the nucleic acid reads in base space. Invarious embodiments, system 300 can be configured to process the nucleicacid sequence reads in flow space. It should be understood, however,that the system 300 disclosed herein can process or analyze nucleic acidsequence data in any schema or format as long as the schema or formatcan convey the base identity and position (or position range) of thenucleic acid sequence within the reference sequence.

In various embodiments, the system 300 can be configured to distinguishbetween positions with a called variant, positions that have been calledas reference, and positions with no call. Positions with a calledvariant can include positions where sufficient evidence was provided bythe reads to indicate the specimen sequence contains a variant.Positions that have been called as reference can include positions wherethere is sufficient evidence to support the conclusion that the specimensequence is substantially identical to the reference sequence at theposition. Positions with no call can include positions where there isinsufficient evidence to determine if the specimen sequence is the sameas or different from the reference sequence. For example, positions withno call can include positions with low coverage, positions with low basequality, or positions where the read sequences indicate different baseswith insufficient homogeneity to determine the sequence with sufficientconfidence. Generally, positions with no call can be indicated asmatching the reference sequence and may be excluded from reporting ofvariants. However, for positions where the reference sequence hasparticular functional or clinical significance, a no call may beindicated on the report. For example, if a treatment has been foundeffective for individuals matching the reference sequence at aparticular position but is contraindicated for individuals with certainvariants at the position, a no call at the position can be indicated ina report. Thus, a clinician reviewing the report may determine that thetreatment should be avoided without further evidence rather than relyingon an indication that the position matches the reference sequence simplybecause no variant was identified.

FIG. 5 is an exemplary flowchart showing a method 500 for annotatinggenomic variants, in accordance with various embodiments.

In step 502, one or more variant calls for a sample genome are receivedfrom a first data source, such as a variome data source. In variousembodiments, the variome data store can be configured to store thevariant calls received from the variant calling engine in a format thatis accessible for mining.

In step 504, functional type annotations are associated to calledvariants that fall within a block of overlapping transcripts (of thesample genome) at the same time, wherein the functional type annotationsare stored in a second data store such as an annotations data store.That is, overlapping transcripts are grouped together into a “geneblock” and then all the called variants in the gene block are annotatedtogether. The advantage here is that multiple called variants that arepotentially mutually interacting can be grouped and annotated togetherto give researchers/clinicians greater insight into the synergistic orantagonistic interplay between variants.

In various embodiments, only called variants that fall within anintragenic region or intron, of the sample genome are annotated. Invarious embodiments, only the called variants in the intergenic regionof the sample genome are annotated.

In step 506, interpretive type annotations are associated to all calledvariants of the sample genome, wherein the interpretive type annotationsare stored in a second data store, such as an annotations data store. Invarious embodiments, only called variants that fall within a codingregion (for example, exons, codons) of the sample genome are annotatedwith the interpretive type annotations. In various embodiments, onlycalled variants that fall within an intragenic region or intron of thesample genome are annotated. In various embodiments, only the calledvariants in the intergenic region of the sample genome are annotated.

In step 508, the annotated called variants are stored in the first datastore, such as a variome data store. In various embodiments, calledvariants are stored after each annotation step. That is, the calledvariants are stored after being functionally annotated and stored againafter the interpretive annotation step.

In step 510, variant report filter conditions are set by a user. Theseare filter conditions that users set to filter out the called variantsthat are included in the called variants summary report that isgenerated in a subsequent step. Examples of filter conditions include,but are not limited to, filtering only for: variants that are non-synonomous and fall within a particular gene, variants that areassociated with a particular disease condition, variants that have afunctional SIFT score of greater or less than a selected value, variantsthat are not present in dbSNP, variants that fall in gene panel regions(defined by user), etc, or combinations thereof.

In various embodiments, the samples, workflows, analyses, annotatedvariants, variant knowledge bases, and the like can be shared with otherusers through a collaboration space. A collaboration space enables thesharing of data with users outside of an organization, collaboration onworkflow development and data analysis, and external review of aworkflow or analysis. For example, cross organization research can usecollaboration space to share data between researchers at differentorganizations. In another example, users can use a collaboration spaceto work with support personnel to define workflows, refine parametersused for various parts of the workflow, review results to diagnosesoftware errors, add additional annotation data sets, and the like. Inyet another example, results of an analysis can be shared with anexternal expert using a collaboration space to get a second opinion oradditional insight as to a set of variants that a user is not familiarwith.

In step 512, the first data store, such as a variome data store, isqueried based on the selected variant report filter conditions.

In step 514, an annotated variant report is generated summarizing theresults of the query in step 512. In various embodiments, the annotatedvariant report can be associated with de-indentified personalinformation. The de-identified personal information may enable aclinician treating a patient to associate the report with the patient.However, the de-identified personal information may be insufficient onits own to associate the report with an individual.

FIG. 6 is an exemplary flowchart showing a method 600 for annotatinggenomic variants, in accordance with various embodiments.

In step 602, the annotation source file can be obtained. The annotationsource file can include a list of genomic coordinates identifying thelocation within the genome corresponding to the annotation.

In step 604, the annotations can be normalized such that the genomiccoordinates reference the same strand of the reference genome, such asthe positive (+) strand.

In 606, an optional anchor base can be added. The anchor base cansignify a normalized position, such as a left most or 5′ position on thepositive (+) strand, to which the variant can be assigned. For example,if the reference sequence contained ATATATAT and a variant sequence hasbeen identified containing ATATAT, the variant could be annotated aseither a TA deletion or an AT deletion. Furthermore, the annotation maybe mapped to many positions within the repeated sequence. As such, ananchor base can be added to the annotation file to indicate the leftmost or 5′ position of the repeated sequence. In various embodiments,the original position of the source annotation can also be maintainedfor future reference. In other embodiments, the anchor base can be atthe right most or 3′ position of the positive (+) strand. Importantly,the genomic coordinate of the anchor base needs to be consistent forboth forward (positive (+) strand) and reverse (negative (−) strand)reads.

In various embodiments, using left most or right most genome coordinatescan cause problems when analyzing the results in translation space.Specifically, in translation space, the relevant affect is the change inamino acid sequence, which occurs at the 3′ end of the coding strand. Inparticular embodiments, when working in translation space, the genomiccoordinates can be converted to the 3′ end of the coding strand asneeded.

In step 608, the annotations can be stored in an annotations database.

In step 610, a set of called variants can be provided. The calledvariants can be assigned positions consistent with the normalizedgenomic coordinates of the annotations. For example, the called variantscan be assigned left most or 5′ positions on the positive (+) strand ofthe reference genome.

In step 612, annotations from the annotations database can be associatedwith the called variants, such as by matching the genomic coordinates ofthe called variants with the genomic coordinates of the annotations. Invarious embodiments, when the user is provided with the annotationsassociated with the called variants, such as in a report, the originalposition of the source annotation can be provided along with the anchorposition.

As discussed above, conventional nucleic acid sequence analysis systemsdo not lend themselves to easy analysis and interpretation of genomicvariant candidates identified in nucleic acid sequencing data. A steptowards rectifying this shortfall is the development of new userinterfaces and methods for graphically displaying and configuringnucleic acid sequence data analysis workflows/pipelines in a clear andeffective manner to allow a researcher/clinician to readily navigatethrough the myriad of data analysis options and configurations.

In various embodiments, various functions required for analyzingspecimen data can be provided. For example, these functions can includeimporting the data, configuring workflows, analyzing specimen data usinga configured workflow, reviewing the results, interpreting thebiological significance of the identified variants, and producingreports. Additionally, multiple roles can be defined. Roles can beassigned one or more functions, and functions can be restricted tospecific roles. For example, an import role, a analyze role, and areport role can be defined. The import role can be assigned thefunctions of importing sample data and performing pre-configuredworkflows, the analyze role can be assigned the functions of configuringa workflow and reviewing the results, and the report role can beassigned the functions of interpreting the biological significance andproducing reports. In particular embodiments, multiple roles can beassigned the same functions. For example, both the analyze role and theimport role can be assigned the tasks of importing and performingpre-configured workflows, while the functions of configuring a workflowand reviewing the results can be restricted to the analyze role. Inparticular embodiments, a user can define custom roles and assignfunctions to the custom roles. Additionally, the roles can be assignedto users such that an individual user can be provided with thecapability to perform certain functions and may not have access to otherfunctions.

FIG. 7 is an exemplary flow diagram 700 illustrating a configuring aworkflow function. At 702, a user can be presented with a login screen.Logins can be based on individual accounts, to which specific roles havebeen granted. For example, by logging in to an account that has beengranted the analyze role, access to the function of configuring aworkflow can be provided.

At 704, the user can be presented with a home page. The home page canpresent the user with links to the functions available to the user, suchas access to configure a workflow.

At 706, the user can be presented with an interface for configuring aworkflow. Completion of the configuration can be dependent on completionof several sub-functions, such as configuring Attributes, Vocabularies,Filters, Annotation Sets, QC Protocols, and Report Templates. Throughthe configure interface, a user can access the sub-functions required toconfigure the workflow. All of these sub-functions can follow aCreate->Save->Publish paradigm to create a new object, save it forreview, and publish it for use by others when it is finalized. Thepublishing function in particular can require authority of an individualwithin the analyze role. The inputs allowed in the Configurations tab,can include but are not limited to: search/advanced search functions toallow a keyword to be used to find a specific report template,checkboxes for activation or inactivation of those items that are notfinalized (published) and are still available to be viewed, edited, orcloned to develop a new item, a button to allow for the creation of anew item, etc.

FIG. 8 provides an exemplary interface for configuring a workflow. Itcan allow direct navigation to the 6 sub-functions (for example,attributes, controlled vocabularies, filters, annotation sets, QCtemplates, report templates) that should be completed before the mainfunction—configuring a workflow—is possible.

At 708, the user can be presented with an interface for configuringattributes that can be used elsewhere throughout the system. Anattribute can define a consistent place to store structured metadataabout a specific object (for example, sample) in the system, such asLibrary, Library Type, Sample, Barcode (Index), File Path, etc.Additionally, attributes can be used to define relation between samples(tumor, normal, mother, father, offspring), connections between a set ofrelations (such as, paired for tumor/normal or trio formother/father/offspring), and specimen types to describe the tissuesource (blood, FFPE, fresh, etc).

At 710, the user can be presented with an interface for configuringcontrolled vocabularies. Controlled vocabularies can normalize the usageof semantic concepts within the system and can facilitate mapping toexternal nomenclature sets. In its simplest form, this can allownormalization across spelling, capitalization, word order, etc.Additionally, relating internal concepts to external nomenclatures suchas HUGO gene names, disease or drug lists, or pathogenicity of a variantcan allow them to be harmonized more easily.

At 712, the user can be presented with an interface for configuringfilters. The filters can be used to refine the variant list for review.The filters can focus on specific aspects of the variant calls, such astheir functional properties (for example, non-synonymous) or theirrelative allele frequency within the sample.

At 714, the user can be presented with an interface for configuringreference genome assemblies. The interface can show the reference genomeassemblies that have been loaded into the system and can allow thecreation (importing) of new reference assemblies. Creating a newreference assembly can include importing a sequence file and configuringgenomic annotations to be used with the sequence file. The genomicannotations can be uploaded or selected from a preexisting annotationssource, such as dbSNP (list of known SNPs from dbSNP at NCBI), COSMIC(associations between variants and cancers in the COSMIC database), OMIM(Associations between variants and Mendelian traits from OMIM/NCBI),Genemodel (the description of a single gene), Geneset (a set of multiplegenes throughout the genome) and VariantKB (the internal variantknowledge base).

At 716, the user can be presented with an interface for configuring QCProtocols. QC Protocols can be used to assess performance of anindividual specimen analysis. QC Protocols can describe the requirementsfor success by defining thresholds for each metric to be used inassessing run quality—sequencing depth, GC bias, strand bias, etc.—andthus the validity of the variant calls derived within that analysis. Theselected criteria can be calculated from the relevant set of input reads(such as, FASTQ, CSFASTQ, or SFF), mapped reads (such as, SAM or BAM),variants (such as VCF) or at other related steps in the processing. Theinterface can include a set of previously defined metrics and allow forthe inclusion/exclusions of individual metrics and setting of tolerancethresholds for each metrics. FIG. 9 illustrates an exemplary interfacefor configuring a QC Protocol.

At 718, the user can be presented with an interface for configuringreport templates. Report templates can allow the customization of thereport structure and describe the way data is to be presented. Forexample, the report template can define where information, such asspecimen details, report type, and results, is presented in the report.

At 720, the user can be presented with an interface for configuringworkflows. Workflows can describe a set of modules (for example, read QCmetrics, read mapping, SNP detection) to be included and configured fora new test within the system. The basic steps to generate a new workfloware: 1. creation of Workflow Details—the high level description of theworkflow, 2. customization of modules—describing which modules will berun and configuring their input parameters, 3. selection of a QCtemplate to certify that the data were generated properly before variantcalling, and 4. selection of a Report Template to format the variantresults for messaging outside the lab.

Once the workflow is configured and published, it can be run on specimensamples by a such as a user assigned the Import role or the Analyzerole. When the results are ready, they are analyzed and reviewed a userwith the Analyze role.

FIG. 10 is an exemplary flow diagram 1000 illustrating the ‘analyze aspecimen’ function. At 1002, a user can be presented with a loginscreen. Logins can be based on individual accounts, to which specificroles have been granted. For example, by logging in to an account thathas been granted the analyze role or the import role, access to thefunction of analyzing a specimen can be provided.

At 1004, the user can be presented with a home page. The home page canpresent the user with links to the functions available to the user, suchas access to analyze a specimen.

At 1006, the user can be presented with an interface for analyzing aspecimen. The interface can direct the user to select a workflow, selectdata (specimen), preview and confirm, and then to launch the analysis.

At 1008, the user can be presented with an interface for importing aspecimen. Importing a specimen can involve specifying the metadata(specimen information) and the data itself (sequence data) that isderived from that specimen. The metadata can be uploaded from a textfile in a specific format, and the sequence data file may be specifiedwith the metadata or may be uploaded separately.

At 1010, the user can be presented with an interface for relatingspecimens. Relating specimens can allow the aggregation of multiplespecimens to be used in a single analysis and can allow their relativeroles to be defined. For example, a trio relation can have threespecimens that are defined to be from the mother, father, and offspring(perhaps self or proband). In various embodiments, more complexpedigrees can be constructed by connecting multiple trio relationstogether through an individual, such as having the individual as anoffspring in one trio and a parent in one or more other trios. Inanother example, a paired relation can have two specimens that aredefined to be from normal tissue and a tumor.

At 1012, the user can be presented with an interface for selecting oneor more specimens for analysis. The interface can include a searchfunction, an advanced search function, a list of available specimens, orother functionality to assist the user in finding and selecting thespecimen for analysis. Additionally, for related specimens, theinterface can provide a way to identify related specimens or canautomatically select related specimens when a first specimen of therelation is selected.

At 1014, the user can be presented with an interface for launching ananalysis. The interface can guide the user through multiplesub-functions for preparing and initiating the analysis. At 1016, theuser can be presented with an interface for selecting a workflow. Forexample, the interface may provide a list of workflows and the user canselect a workflow by clicking on the workflow or a checkbox associatedwith the workflow. At 1018, the user can be presented with an interfacefor selecting the data for analysis. For example, the interface mayprovide a list of specimens or data files associated with selectedspecimens that are available for analysis with the selected workflow. Inparticular embodiments, the list of specimens or data files can befiltered to present only specimens or data files appropriate for theselected workflow. For example, if a paired analysis workflow isselected, the list of specimens or data files may be limited to thosespecimens that have been identified as part of a paired relation.Another example is that reads can be required for workflows containing amapping component as the data type should be compatible with theworkflow; if input data is VCF (variants), this is not appropriate for amapping workflow. At 1020, the user can be presented with an interfacefor previewing and confirming the selected analysis.

At 1022, the user can be presented with an interface for reviewing thestatus of analyses. The interface can display the status of currentlyrunning analyses and identify analyses that successfully completed orthat failed, such as by failing the associated QC Protocol.Additionally, the interface can identify analyses that have been queuedbut have not yet launched.

FIG. 11 is an exemplary flow diagram 1100 illustrating the ‘publish areport’ function. At 1102, a user can be presented with a login screen.Logins can be based on individual accounts, to which specific roles havebeen granted. For example, by logging in to an account that has beengranted the report role, access to the function of publish a report canbe provided.

At 1104, the user can be presented with a home page. The home page canpresent the user with links to the functions available to the user, suchas access to publish a report. The ‘publish a report’ function candirect the user to select an analysis (specimen), review and filtervariants and annotations, and then to publish the report.

At 1106, the user can be presented with an interface for finding ananalysis for review. The interface can provide a search function, anadvanced search function, a list of analyses available for review, orother functionality to enable the user to find and select an analysisfor review. In various embodiments, the interface can provide a list ofsamples for which the annotation is complete and are available forpreparing a report. Additionally, the interface can provide anindication of which stage the report is in. For example, clicking on aplus sign by the sample name can expand the list to provide the stage ofindividual analysis. Stages that are greyed out are may not completed.The current stage can be the last ungreyed stage in the list.

At 1108, the user can check out the analysis for review. By checking outthe analysis, the system can limit the ability of multiple users fromworking on the same analysis or report.

At 1110, the user can select single sample variant filters. Singlesample variant filters can be applied to select, for example, variantsthat have a higher likelihood of being clinically significant. Thevariants may be filtered by disease, gene panel, variant type, database,values of functional predictions, etc.

At 1112, the user can select multi sample variant filters. Multi samplevariant filters can be applied to, for example, a paired analysis, suchas with Tumor/Normal pairs, or a Trio, such as a set ofMother/Father/Child. Tumor/Normal pairs typically represent specimensfrom two different tissues within a single individual. The normal is asomewhat ‘matched’ control—best if it is a specimen from the ipsilateraltissue (other side of the body), but this may vary with access to‘normal’ tissue. Trios are sets of Mother/Father/Child specimens,usually germline, that are used to detect de novo mutations (presentonly in the child) or Mendelian Inheritance inconsistencies. Multisample variant filters can be used to select variants that are common tomore than one specimen, or variants that are unique to a single specimenof the group. For example, a paired analysis can be filtered to selectvariants that are unique to tumor tissue.

In various embodiments, paired analysis can provide an indication ofwhich variants are unique to a tumor sample and which variants arecommon to the tumor sample and a normal control sample. Identifyingvariants unique to the tumor sample can aid in identifying therapiesthat are effective against the tumor. Additionally, identifying variantscommon to the tumor and the normal control sample, or variants that areunique to the control sample, can aid in identifying therapies thatminimize side effects for a patient. Alternatively, in a researchsetting, identifying variants that are unique to the tumor can provideinsight on tumor progression and mechanisms for cancer development.

In various embodiments, and interface showing a Venn diagram displayingthe variants that are common or are shared between the three members ofa trio (mother/father/child) or a paired sample (Tumor/Normal) can beprovided to assist the user in easily identifying variants that areeither unique or in common between pairs or sets of samples. Forexample, de novo mutations would be found in the child but not theparents in trios, or somatic mutations would be found in the tumorspecimen but not its matched normal control. In various embodiments, thetrio representation can be expanded to include more complex pedigrees.

In various embodiments, variants from either single or multi sampleanalysis can be filtered based on their position relative to features(for example, genes or regions). FIG. 12A illustrates an exemplaryinterface showing that each gene panel is a non-overlapping collectionof genomic regions that describe either the structures of single genesor an intergenic region of interest. When variant analysis is performed,variants may be found in some of these regions but not in others. Thiscan enable partitioning of the gene panel into regions With Variants andregions Without Variants, which are mutually exclusive.

In various embodiments, the variants can be filtered base on afunctional prediction score. For example, SIFT, PolyPhen, and Granthamprovide ways of assessing the effect of a particular amino acid changeon the function or effectiveness of the protein. Typically the scoresrange from no effect (for example synonymous nucleotide change that doesnot affect the amino acid choice or a nonsynonymous nucleotide changebetween two amino acids with very similar properties like Lysine andArginine) to a strong effect (introduction of a stop codon, creation orobliteration of a splicing site, change of an amino acid from small tolarge within a folded protein, change of an amino acid frompolar/charged to non-polar/non-charged on the surface of the protein, achange to or from a cystine). For example, an interface can provide theuser with slider to allow the selection of a range of scores to be usedin the filtering process. FIG. 12B illustrates an exemplary interfacefor setting filters.

When the user has selected the appropriate filters and chosen theappropriate settings for the filters, the user can select to generate areport. In various embodiments, a selection of filters and theirsettings can be saved to be used to generate similar reports for otheranalysis. At 1114, the user can be presented with a preview of thereport. Additionally, the user may add comments or a summary. Uponapproval of the report, the user can publish the report at 1116.

FIG. 13 is an exemplary flowchart showing a method 1300 for generating areport, in accordance with various embodiments.

In step 1302, one or more variants are selected from a first datasource, such as a variome data source. In various embodiments, thevariome data store can be configured to store the variant in a formatthat is accessible for mining. In various embodiments, the variants canbe selected by using filtering criteria to identify variants relevant tothe report.

In step 1304, annotations associated with the selected variants can bereceived, and, in step 1306, sentence templates corresponding to theannotations can be identified. A sentence template can be a sentencestructure with portions of the sentence defined and other portions ofthe sentence to be defined based on values associated with the variantor the annotation. For example, “(variant identifier) is in (geneidentifier)” where the variant identifier and the identifier can bepopulated based on the variant and the annotation, or “(gene identifier)has been found to be related to (disease state) by (reference citation)”where the gene identifier, disease state, and reference citation can bepopulated based on variant and annotation information. In variousembodiments, general sentence templates can be defined to correspond todifferent annotation types, such as by defining a functional typeannotation sentence template and an interpretive type annotationsentence template. Further, sentence templates can be defined based onthe level of annotation, such as allele level sentence template, genelevel sentence templates, transcript level sentence templates, and thelike. Still further, specific sentence templates can be defined forindividual annotations or groups of annotations.

In step 1308, grammar rules can be applied to build the sentences. Forexample, grammar rules can be defined to select an appropriate articlebased on the information being inserted into a sentence template.Similarly, grammar rules can be defined to select an appropriate verbdepending on whether an inserted noun is singular or plural. The grammarrules can be defined generally to apply to a group of sentence templatesor a group of annotations, or specific grammar rules can be defined tomake appropriate selections for problematic annotations.

In step 1310, paragraphs can be generated using annotations and thecorresponding templates. For example, multiple sentence templates can bepopulated with the required information and structured into a paragraph.In various embodiments, paragraph rules can define how the sentencetemplates are arranged into the paragraph, such as which sentencetemplates occur earlier in the paragraph thereby defining a logicalprogression in the information or grouping of sentences by annotationsource, specificity (such as allele, locus, transcript, gene, or thelike), relevance, etc. For example, a sentence for identifying a genemay be required to be located before a sentence providing informationabout the gene, and sentences related to annotations from one annotationsource may be grouped separately from sentences related to annotationsfrom another annotation source.

Additionally, multiple paragraphs can be generated based on variousgroupings of annotations. For example, an allele paragraph can begenerated to include allele level annotations for variants associatedwith an allele. Additionally, locus paragraphs, transcript paragraphs,gene paragraphs, etc, can be generated for relevant groups of variantsto include annotation information relevant to the respective levels. Forexample, a gene paragraph can be generate to identify a gene in whichone or more variants were identified and selected, and to provideinformation about the gene relevant to the report, rather than repeatingthe identity of the gene and the relevant information for each selectedvariant. In various embodiments, separate paragraphs can be generatedfor each annotation source, for each level of relevance, other groupingsof sentences, or any combination thereof.

In step 1312, a report containing the paragraphs can be provided to auser, such as for review and editing, or for publication.

FIG. 14 illustrates an exemplary interface for viewing the status of anaccount. From the status interface, a user can view the number ofanalyses that are running, complete, or failed. Further, the user canview the number of samples where an analysis has been launched, thenumber of samples where an analysis has not been launched, and thenumber of samples that have been archived. The status interface can alsoprovide an indication of which collaboration spaces are active, andaccount balances.

In various embodiments, sets of general sentence templates can bepredefined, and a user can define additional sentence templates, such asbased upon review of the identified variants and resulting reports. Forexample, general sentence templates can be predefined to generate areport providing information related to the identified variants and userdefined sentence templates can be defined to highlight significantdiagnostic information when a particular variants is identified.Similarly, in various embodiments, sets of general grammar and paragraphrules can be predefined and the user can define additional grammar rulesbased upon review of the resulting reports. For example, the user maynotice that the general grammar rules perform poorly in selecting anappropriate article for a particular annotation and may define aspecific grammar rule to correctly select the article for thatannotation. In various embodiments, new templates and rules can bedefined by entering a template or rule or new templates and rules can beautomatically generated by the system when a report is edited. Inparticular embodiments, when the templates or rules are automaticallygenerated, the user may be presented with the automatically generatetemplate or rule and given the option to modify, discard, or save theautomatically generated template or rule.

In various embodiments, the methods of the present teachings may beimplemented in a software program and applications written inconventional programming languages such as C, C++, etc.

While the present teachings are described in conjunction with variousembodiments, it is not intended that the present teachings be limited tosuch embodiments. On the contrary, the present teachings encompassvarious alternatives, modifications, and equivalents, as will beappreciated by those of skill in the art.

Further, in describing various embodiments, the specification may havepresented a method and/or process as a particular sequence of steps.However, to the extent that the method or process does not rely on theparticular order of steps set forth herein, the method or process shouldnot be limited to the particular sequence of steps described. As one ofordinary skill in the art would appreciate, other sequences of steps maybe possible. Therefore, the particular order of the steps set forth inthe specification should not be construed as limitations on the claims.In addition, the claims directed to the method and/or process should notbe limited to the performance of their steps in the order written, andone skilled in the art can readily appreciate that the sequences may bevaried and still remain within the spirit and scope of the variousembodiments.

The embodiments described herein, can be practiced with other computersystem configurations including hand-held devices, microprocessorsystems, microprocessor-based or programmable consumer electronics,minicomputers, mainframe computers and the like. The embodiments canalso be practiced in distributing computing environments where tasks areperformed by remote processing devices that are linked through anetwork.

It should also be understood that the embodiments described herein canemploy various computer-implemented operations involving data stored incomputer systems. These operations are those requiring physicalmanipulation of physical quantities. Usually, though not necessarily,these quantities take the form of electrical or magnetic signals capableof being stored, transferred, combined, compared, and otherwisemanipulated. Further, the manipulations performed are often referred toin terms, such as producing, identifying, determining, or comparing.

Any of the operations that form part of the embodiments described hereinare useful machine operations. The embodiments, described herein, alsorelate to a device or an apparatus for performing these operations. Thesystems and methods described herein can be specially constructed forthe required purposes or it may be a general purpose computerselectively activated or configured by a computer program stored in thecomputer. In particular, various general purpose machines may be usedwith computer programs written in accordance with the teachings herein,or it may be more convenient to construct a more specialized apparatusto perform the required operations.

Certain embodiments can also be embodied as computer readable code on acomputer readable medium. The computer readable medium is any datastorage device that can store data, which can thereafter be read by acomputer system. Examples of the computer readable medium include harddrives, network attached storage (NAS), read-only memory, random-accessmemory, CD-ROMs, CD-Rs, CD-RWs, magnetic tapes, and other optical andnon-optical data storage devices. The computer readable medium can alsobe distributed over a network coupled computer systems so that thecomputer readable code is stored and executed in a distributed fashion.

What is claimed is:
 1. A system, comprising: a first data storeconfigured to store genetic sequence information comprising calledvariants; a second data store configured to store sequence annotationdata; an annotations component communicatively connected with the firstdata store and the second data store, comprising: a functionalannotations engine configured to: receive the called variants from thefirst data store, and associate functional type annotations from thesecond data store with the called variants, and an interpretiveannotations engine configured to: receive the called variants from thefirst data store, and associate interpretive type annotations from thesecond data store with the called variants; a reporting modulecommunicatively connected with the first data store and the second datastore and configured to generate a report of the called variants, thefunctional annotations, and the interpretive annotations.
 2. A system ofclaim 1, wherein the functional type annotation includes an indicationof a change in an amino acid sequence, an indication of a change in anexpression level of a protein, an indication of a change in the splicingof a transcript, or any combination thereof.
 3. A system of claim 1,wherein the functional-type annotations includes a listing oftranscripts impacted by the called variant.
 4. A system of claim 3,wherein the functional-type annotations includes a protein functionimpact score for the called variant.
 5. A system of claim 4, wherein thefunctional-type annotations includes base information for codons withthe called variant.
 6. A system of claim 1, wherein the interpretivetype annotation includes an association of a variant with a disease, ancorrelation between a variant and a response to a treatment, metabolicpathways impacted by the called variant, biological signaling pathwayimpacted by the called variant, regulation pathway impacted by thecalled variant, a match to a list of annotated variants, or acombination thereof.
 7. A system of claim 1, wherein the interpretivetype annotation includes a metabolic pathways impacted by the calledvariant, a biological signaling pathway impacted by the called variant,a regulation pathway impacted by the called variant, or a combinationthereof.
 8. A system of claim 1, wherein the called variants that fallwithin blocks of overlapping transcripts are annotated at the same time.9. A system of claim 1, further comprising a filtering component incommunications with the first data source and configured to query thefirst data store based a set of variant filter conditions and whereinthe report summarizes results of the query.
 10. The system of claim 1,further comprising: an annotations importer component in communicationswith the second data store and configured to convert annotationsinformation received from external annotations sources to a format thatcan be stored on the second data store.
 11. A computer implementedmethod, comprising: receiving the called variants from a first datastore configured to store genetic sequence information comprising calledvariants, and associating the called variants with functional typeannotations from the second data store configured to store sequenceannotation data, and associating the called variants with interpretivetype annotations from the second data store; generating a report of thecalled variants, the functional annotations, and the interpretiveannotations; and providing the report to a first user
 12. The computerimplemented method of claim 11, further including: selecting variantreport filter conditions; querying the first data store based on theselected variant report filter conditions; and wherein the reportsummarizes the results of the query.
 13. The method of claim 11, furthercomprising receiving instructions from the first user to modify thereport.
 14. The method of claim 13, wherein a second user is restrictedfrom modifying the report.
 15. The method of claim 11, furthercomprising receiving instructions from the first user to publish thereport.
 16. The method of claim 14, wherein a second user is restrictedfrom publishing the report.
 17. The method of claim 11, furthercomprising receiving instructions from a second user to associate thecalled variants with the functional type annotations or to associate thecalled variants with the interpretive type annotations.
 18. The methodof claim 17, wherein the first user is of a first class of users and thesecond user is of a second class of users.
 19. A system, comprising: afirst data store configured to store genetic sequence informationcomprising called variants; a second data store configured to storesequence annotation data; an annotations component communicativelyconnected with the first data store and the second data store,comprising: an annotations engine configured to: receive the calledvariants from the first data store, and associate annotations from thesecond data store with the called variants, and a reporter modulecommunicatively connected with the first data store and the second datastore and configured to: select sentence templates corresponding toassociated annotations; generate report paragraphs based on theannotations and the selected sentence templates; and provide a reportincluding the report paragraphs for the called variants and theassociated annotations.